def setParams2D(self, type, vertices, center=False):
"""Set the vertices for a given particle type.
Args:
type (str): Name of the type to set the shape of
vertices (list): List of (2D) points specifying the coordinates of the shape
center (bool): If True, subtract the center of mass of the shape from the vertices before setting them for the shape
Shapes are specified as a list of 2D coordinates. Edges will
be made between all adjacent pairs of vertices, including one
between the last and first vertex.
"""
itype = hoomd.context.current.system_definition.getParticleData().getTypeByName(type);
if not len(vertices):
vertices = [(0, 0)];
center = False;
# explicitly turn into a list of tuples
if center:
vertices = [(float(p[0]), float(p[1])) for p in utils.center(vertices)];
else:
vertices = [(float(p[0]), float(p[1])) for p in vertices];
# update the neighbor list
rcutmax = 2*(sqrt(max(x*x + y*y for (x, y) in vertices)) + self.radius*2**(1./6));
self.r_cut = max(self.r_cut, rcutmax);
self.vertices[type] = vertices;
self.cpp_force.setRcut(self.r_cut);
self.cpp_force.setParams(itype, vertices);
def setParams3D(self, type, vertices, faces, center=False):
"""Set the vertices for a given particle type.
Args:
type (str): Name of the type to set the shape of
vertices (list): List of (3D) points specifying the coordinates of the shape
faces (list): List of lists of indices specifying which coordinates comprise each face of a shape.
center (bool): If True, subtract the center of mass of the shape from the vertices before setting them for the shape
Shapes are specified as a list of coordinates (`vertices`) and
another list containing one list for each polygonal face
(`faces`). The elements of each list inside `faces` are
integer indices specifying which vertex in `vertices` comprise
the face.
"""
itype = hoomd.context.current.system_definition.getParticleData(
).getTypeByName(type)
if not len(vertices):
vertices = [(0, 0, 0)]
faces = []
center = False
# explicitly turn into python lists
if center:
vertices = [(float(p[0]), float(p[1]), float(p[2]))
for p in utils.center(vertices, faces)]
else:
vertices = [(float(p[0]), float(p[1]), float(p[2]))
for p in vertices]
faces = [[int(i) for i in face] for face in faces]
# update the neighbor list
rcutmax = 2 * (
sqrt(max(x * x + y * y + z * z
for (x, y, z) in vertices)) + self.radius * 2**(1. / 6))
self.r_cut = max(self.r_cut, rcutmax)
self.vertices[type] = vertices
self.cpp_force.setRcut(self.r_cut)
self.cpp_force.setParams(itype, vertices, faces)
